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  • Unclear exon-exon connection after RSubjunc() usage

    Hi there.

    I posted this already somewhere else but didn't get any reply. (https://support.bioconductor.org/p/9156811/)

    "
    on my way to address alternatively used exons in a bulkRNAseq dataset I used fastq files and aligned reads with Rsubjunc (see in code below).

    To get a first impression I fed in the bam files of our control into IGV and looked a gene I know from from earlier studies and was surprised to see that the end of the transcript is split, as if the C-terminus was not connected on mRNA level. This confused be because the mRNA should be connected. Is there something, a setting, or something else I am missing here?

    I merged all six bam files in hope the merged file get more read connecting Ex45 with Ex46 (Total exon count is 48).

    Additionally, quiet a few reads are also found in the intronic regions, although not connected enough to say this is intron retention?

    I am happy to hear your opinion on this.

    Code:
    fastq_files <- list.files("../fastq/raw/", full.names = T, include.dirs = F)
    fastq_files_abs <- normalizePath(fastq_files)
    
    subjunc(index = "/home/chuddy/bioinformatics/ref_genomes/mouse_38/genome/subread/GRCm38",
    nthreads = 20,
    readfile1 = fastq_files_abs,
    sortReadsByCoordinates = TRUE)
    
    
    > sessionInfo( )
    R version 4.3.2 (2023-10-31)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 20.04.6 LTS
    
    Matrix products: default
    BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
    LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
    
    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_CH.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
    
    time zone: Europe/Zurich
    tzcode source: system (glibc)
    
    attached base packages:
    [1] grid stats graphics grDevices utils datasets methods base
    
    other attached packages:
    [1] gridExtra_2.3 Rsubread_2.14.2 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
    [8] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0
    
    loaded via a namespace (and not attached):
    [1] Matrix_1.6-5 gtable_0.3.4 compiler_4.3.2 tidyselect_1.2.0 scales_1.3.0 lattice_0.22-5
    [7] R6_2.5.1 generics_0.1.3 knitr_1.45 munsell_0.5.0 pillar_1.9.0 tzdb_0.4.0
    [13] rlang_1.1.3 utf8_1.2.4 stringi_1.8.3 xfun_0.41 timechange_0.3.0 cli_3.6.2
    [19] withr_3.0.0 magrittr_2.0.3 rstudioapi_0.15.0 hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5
    [25] glue_1.7.0 fansi_1.0.6 colorspace_2.1-0 tools_4.3.2 pkgconfig_2.0.3
    ​
    "

    Snippet below. I tried to use other bam files, where STAR was used and it worked and i used Rsubread with GTF annotation file support during mapping and there is also connects the exons.
    I wonder why such a good exon-exon connection is missed by Rsubread when no GTF file is used to help with mapping?
    ​​

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